BN1308 Genetic Spatial Mapping Report

Genetic Spatial Mapping Plot

This plot shows the spatial genetic mapping results across different tissues.

Cauchy Combination Result

This table presents the results of the Cauchy combination test, summarizing the genetic associations.

Annotation P Cauchy P Median
Layer 4 1.6093e-07 3.5813e-05
Layer 5 6.9476e-05 4.4790e-04
Layer 6 2.9470e-04 4.5045e-03
Layer 3 6.2930e-04 2.5431e-02
Layer 2 4.4386e-03 5.9392e-02
Layer 1 8.2764e-02 4.4454e-01
WM 9.9987e-01 5.7998e-01

Diagnosis Manhattan Plot

The Manhattan plot shows the association of SNPs with the top associated gene across the genome.

Gene Expression and GSS Distribution

Select a gene to view its expression distribution and gene specificity score (GSS).

Expression Distribution
TUBB Expression Distribution
Gene Specificity Score (GSS)
TUBB GSS Distribution

Top 50 Gene Diagnostic Info

This table lists the top 50 genes based on diagnostic criteria, including the gene specificity score (GSS) and PCC.

Gene Annotation Median GSS PCC
TUBB Layer 5 3.4160 0.8181
STXBP1 Layer 4 3.2891 0.8147
STMN2 Layer 5 3.4238 0.8146
EEF1A2 Layer 5 3.0586 0.8111
CHGA Layer 4 3.6719 0.8109
YWHAE Layer 4 3.0000 0.8104
STMN1 Layer 4 3.1660 0.8061
VPS35 Layer 4 2.9932 0.8056
ATP1B1 Layer 5 3.1797 0.8051
RTN3 Layer 5 3.0996 0.8030
SOD1 Layer 4 3.0889 0.8030
YWHAG Layer 5 3.1738 0.8028
PRKAR1B Layer 5 3.1523 0.8008
ENO2 Layer 5 3.3574 0.8006
CELF4 Layer 4 3.1250 0.8004
ARPP19 Layer 5 2.9531 0.7995
TSPAN7 Layer 5 2.9531 0.7986
USP22 Layer 5 3.1113 0.7985
RTN1 Layer 5 3.1934 0.7972
RTN4 Layer 5 3.0527 0.7958
MORF4L1 Layer 5 3.0996 0.7954
NEUROD2 Layer 4 3.1055 0.7953
OAZ1 Layer 5 3.0312 0.7948
NSF Layer 5 3.3496 0.7947
KLC1 Layer 5 3.1602 0.7946
APLP1 Layer 5 2.8457 0.7927
SNRPN Layer 5 3.1875 0.7925
DNM1 Layer 5 3.2012 0.7916
YPEL3 Layer 4 2.9336 0.7901
FXYD6 Layer 5 3.2422 0.7899
CLIP3 Layer 5 2.9727 0.7898
SERINC1 Layer 5 3.1113 0.7891
ITM2B Layer 4 3.0088 0.7889
TUBA1A Layer 4 2.9053 0.7888
SPTAN1 Layer 5 2.9023 0.7881
ATP5F1B Layer 5 3.2500 0.7878
SV2A Layer 5 3.0059 0.7876
CABP1 Layer 5 2.9668 0.7875
EIF4A2 Layer 5 3.1191 0.7875
NORAD Layer 5 3.1738 0.7869
UQCRH Layer 4 3.0527 0.7866
TAGLN3 Layer 5 3.1113 0.7862
PKM Layer 5 3.0254 0.7859
YWHAH Layer 5 3.2930 0.7852
SYP Layer 5 3.1191 0.7851
APBB1 Layer 5 3.2930 0.7850
VSNL1 Layer 5 3.2012 0.7846
TLE5 Layer 4 2.9053 0.7845
PREPL Layer 5 3.4902 0.7842
NAPB Layer 5 3.3066 0.7836

Running Info

Click to view detailed run information and parameters.

gsMap Version: 1.73.0

Parameters:

  • Sample Name: BN1308
  • Trait Name: PD
  • Summary Statistics File: /mnt/data/projects/ASAP/ST/gsMAP/GWAS_nallsEtAl2019_allSamples_allVariants.sumstats.gz
  • HDF5 Path: /mnt/data/projects/ASAP/ST/gsMAP/st_anndata_h5ads/st_adata_BN1308_for_gsmap.h5ad
  • Annotation: smoothed_label_s5
  • Spatial LDSC Save Directory: /mnt/data/projects/ASAP/ST/gsMAP/st_mtg_out/BN1308/spatial_ldsc
  • Cauchy Directory: /mnt/data/projects/ASAP/ST/gsMAP/st_mtg_out/BN1308/cauchy_combination
  • Report Directory: /mnt/data/projects/ASAP/ST/gsMAP/st_mtg_out/BN1308/report/PD
  • gsMap Report File: /mnt/data/projects/ASAP/ST/gsMAP/st_mtg_out/BN1308/report/PD/BN1308_PD_gsMap_Report.html
  • Gene Diagnostic Info File: /mnt/data/projects/ASAP/ST/gsMAP/st_mtg_out/BN1308/report/PD/BN1308_PD_Gene_Diagnostic_Info.csv
  • Report Generation Date: 2025-04-11 03:15:51
  • Number of Processes: 10
  • Spending Time: 0h 3m